\Header{processArrayDataObject}{Automated processing and normalisation of an arrayData-object
(part of function processArrayData)}
\keyword{utilities}{processArrayDataObject}
\begin{Description}\relax
Automated processing and normalisation of an
\code{\Link{arrayData}}-object.
The function is called
by \code{\Link{processArrayData}}.
\end{Description}
\begin{Usage}
\begin{verbatim}processArrayDataObject(arrayDataObject, spotIdentifier = "Name", verbose = TRUE, normalisationMethod = "vsn", subtractBackground=FALSE, spotsRemovedBeforeNormalisation = NULL, spotsRemovedAfterNormalisation = NULL, subGroups = NULL, channelsSeparately = FALSE, hybridisationGroups = NULL)\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{arrayDataObject}] object of class \code{\Link{arrayData-class}};
required; default missing

\item[\code{spotIdentifier}] character string; required; default "Name".
\code{spotIdentifier} specifies the column
in the image analysis result files which contain
spot or gene identifiers.
\item[\code{verbose}] logical; required; default: \code{TRUE} 
\item[\code{normalisationMethod}] character string; required; default: "vsn";
cf. argument \code{method} of \code{\Link{normalise}} 
\item[\code{subtractBackground}] logical; required; default: \code{FALSE}
cf. \code{\Link{normalise}} 
\item[\code{spotsRemovedBeforeNormalisation}] vector of character strings;
required; default \code{NULL}.
All spots which match the string(s) will be excluded  
already before normalisation and will not be present
in the resulting objects at all.

\item[\code{spotsRemovedAfterNormalisation}] vector of character strings;
required; default: \code{NULL};
cf. argument \code{spotsRemovedBeforeNormalisation}

\item[\code{subGroups}] character string or \code{NULL};
required; cf. \code{\Link{normalise}};
default: \code{NULL} 
\item[\code{channelsSeparately}] logical; required;
cf. \code{\Link{normalise}};
default: \code{FALSE}
\item[\code{hybridisationGroups}] list of numeric vectors;
cf. \code{\Link{normalise}};
required; default: \code{NULL}
\end{ldescription}
\end{Arguments}
\begin{Value}
A list of objects, i.e.  an "exprSetRGObject" and and
"arrayDataObject" with corresponding class types
\code{\Link{exprSetRG-class}} and
\code{\Link{arrayData-class}}.
\end{Value}
\begin{Author}\relax
Andreas Buness <a.buness@dkfz.de>
\end{Author}
\begin{SeeAlso}\relax
\code{\Link{processArrayData}},
\code{\Link{normalise}},
\code{\Link{exprSetRG-class}},
\code{\Link{arrayData-class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
       LOADPATH <- file.path(.path.package("arrayMagic"), "extdata")
        SLIDEDESCRIPTIONFILE <- "slideDescription"

       slideDescription <- readpDataSlides(
                             loadPath=LOADPATH, 
                             slideDescriptionFile=SLIDEDESCRIPTIONFILE
                           )
        arrayDataObject <- readIntensities(
                             loadPath=LOADPATH,
                             slideDescription=slideDescription
                          )

       resultList <- processArrayDataObject( arrayDataObject=arrayDataObject )
         
 \end{ExampleCode}
\end{Examples}

